I have download the “tem2_with_everything_HSE_8mhz fixed SHORTENED.zip (443.35 Kb)” file. The STM32CubeMX-generated code was for TrueSTUDIO and not System Workbench.
I did download the latest version of STM32CubeMX (v4.7.0), opened your project and change the Toolchain/IDE to SW4STM32 in the project settings. Then I’ve regenerated the code.
On System Workbench, I chosed the CubeMX project root directory as workspace, then imported the generated project.
To debug, I have found the debug script “nucleo-f411re.cfg” in the repertory “SystemWorkbench\plugins\fr.ac6.mcu.debug_188.8.131.52503121050\resources\openocd\scripts\st_board”. I’ve copied it into the project and select it as local script in the debug configuration.
My workspace is attached in http://dl.free.fr/k9pDN3ZlN. Run System Workbench with this fiolder as workspace. You should see your project.
Hope it will work and help you.